rs11102091

chr1-110332802-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_036595.1(RBM15-AS1):n.175+6195T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,860 control chromosomes in the GnomAD database, including 26,139 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (26139 hom., cov: 30)
• Consequence: RBM15-AS1 NR_036595.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915

Genes affected

RBM15-AS1 (HGNC:53636): (RBM15 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM15-AS1	NR_036595.1	n.175+6195T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM15-AS1	ENST00000449169.1	n.175+6195T>C		intron_variant, non_coding_transcript_variant		1
RBM15-AS1	ENST00000686992.1	n.157+6195T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88768 AN: 151742 Hom.: 26126 Cov.: 30

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.558

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.585 AC: 88834 AN: 151860 Hom.: 26139 Cov.: 30 AF XY: 0.581 AC XY: 43111 AN XY: 74194

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.557

Alfa AF: 0.580 Hom.: 6378

Bravo AF: 0.593

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11102091; hg19: chr1-110875424;